spliceEvent {ribosomeProfilingQC} | R Documentation

## Get splicing events

### Description

Get differentical usage of alternative Translation Initiation Sites, alternative Polyadenylation Sites or alternative splicing sites

### Usage

    spliceEvent(coverage, group1, group2)

### Arguments

`coverage` | Coverages of feature region with extensions. Output of coverageDepth
`group1, group2` | The sample names of group 1 and group 2

### Value

A GRanges object of splice events.

### Examples

    ## Not run:
    path <- system.file("extdata", package="ribosomeProfilingQC")
    RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
    gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    coverage <- coverageDepth(RPFs, gtf=gtf,
                      level="gene", region="feature with extension")
    group1 <- c("RPF.KD1.1", "RPF.KD1.2")
    group2 <- c("RPF.WT.1", "RPF.WT.2")
    se <- spliceEvent(coverage, group1, group2)

    ## End(Not run)

[Package ribosomeProfilingQC version 0.99.9 Index]